[BioC] DEXSeq dispersion trend estimation?

[Alejandro Reyes]

Hi Ryan,

Thanks for your e-mail!

For all previous versions, the dispersion-mean trend was done using the 
mean for a given exon. The latest version on the svn is including the 
sum of counts from the other exons, but this is not optimal, since (as 
you mention) the mean of the counts get inflated and each exon from the 
same gene would have the same mean, for some cases, this causes the 
dispersion-mean trend not to be obvious.  We will change it soon in the 
next commit of the svn, the reason we have not done it is because when 
doing it we encounter some problems with the running times in subsequent 
steps... my feeling is that it is a strange behavior of the GLM fitter, 
and  I already contacted the maintainer, so it is work in progress!

Will keep you updated,
Alejandro Reyes


> Hello,
>
> I am trying to understand the methods used in DEXSeq, and I was hoping 
> you could clear up some of the details of the dispersion trend 
> squeezing strategy. In particular, when fitting the dispersion-mean 
> trend, what is used as the mean for a given exon? Is this computed 
> only based on the exon's own counts, or is it the mean of all the 
> counts for that exon, including the sum of counts in other exons? If 
> it is the latter, wouldn't the mean be identical for every exon in the 
> same gene, since the total counts for that gene are constant, and if 
> so, is this the intended effect?
>
> Thanks,
>
> -Ryan Thompson